This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.
Testing the association between mutation status of 120 genes and 7 molecular subtypes across 155 patients, 12 significant findings detected with P value < 0.05 and Q value < 0.25.
-
BRAF mutation correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', and 'CN_CNMF'.
-
TP53 mutation correlated to 'CN_CNMF'.
-
FAT4 mutation correlated to 'CN_CNMF'.
-
FLG mutation correlated to 'MRNA_CNMF' and 'CN_CNMF'.
-
DNAH5 mutation correlated to 'MRNA_CNMF'.
-
CASP8 mutation correlated to 'MRNA_CHIERARCHICAL'.
-
ZC3H13 mutation correlated to 'MRNA_CHIERARCHICAL'.
-
SYNE1 mutation correlated to 'MRNA_CNMF' and 'CN_CNMF'.
Table 1. Get Full Table Overview of the association between mutation status of 120 genes and 7 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 12 significant findings detected.
Clinical Features |
MRNA CNMF |
MRNA CHIERARCHICAL |
CN CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
||
nMutated (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
BRAF | 20 (13%) | 135 |
5.58e-06 (0.00454) |
8.43e-08 (6.87e-05) |
8.5e-05 (0.0689) |
0.734 (1.00) |
0.926 (1.00) |
0.145 (1.00) |
1 (1.00) |
FLG | 26 (17%) | 129 |
0.000232 (0.188) |
0.00927 (1.00) |
0.00027 (0.218) |
0.232 (1.00) |
0.252 (1.00) |
1 (1.00) |
0.61 (1.00) |
SYNE1 | 37 (24%) | 118 |
0.000146 (0.118) |
0.000472 (0.379) |
0.000289 (0.232) |
0.729 (1.00) |
0.78 (1.00) |
1 (1.00) |
0.181 (1.00) |
TP53 | 75 (48%) | 80 |
0.00371 (1.00) |
0.00883 (1.00) |
1.08e-09 (8.81e-07) |
0.403 (1.00) |
0.38 (1.00) |
0.366 (1.00) |
0.807 (1.00) |
FAT4 | 29 (19%) | 126 |
0.0176 (1.00) |
0.0068 (1.00) |
0.000172 (0.14) |
0.419 (1.00) |
0.322 (1.00) |
0.241 (1.00) |
0.0218 (1.00) |
DNAH5 | 28 (18%) | 127 |
4.26e-06 (0.00347) |
0.00131 (1.00) |
0.0134 (1.00) |
0.693 (1.00) |
0.12 (1.00) |
0.585 (1.00) |
0.642 (1.00) |
CASP8 | 10 (6%) | 145 |
0.000518 (0.415) |
1.21e-05 (0.00979) |
0.00174 (1.00) |
0.0587 (1.00) |
0.208 (1.00) |
1 (1.00) |
0.255 (1.00) |
ZC3H13 | 17 (11%) | 138 |
0.00144 (1.00) |
0.000266 (0.215) |
0.00682 (1.00) |
0.281 (1.00) |
0.0214 (1.00) |
1 (1.00) |
0.41 (1.00) |
APC | 103 (66%) | 52 |
0.0438 (1.00) |
0.0286 (1.00) |
0.101 (1.00) |
0.7 (1.00) |
0.388 (1.00) |
1 (1.00) |
1 (1.00) |
FBXW7 | 29 (19%) | 126 |
0.176 (1.00) |
0.109 (1.00) |
0.000825 (0.658) |
0.00533 (1.00) |
0.233 (1.00) |
0.583 (1.00) |
0.657 (1.00) |
KRAS | 58 (37%) | 97 |
0.00324 (1.00) |
0.000947 (0.754) |
0.15 (1.00) |
0.772 (1.00) |
0.752 (1.00) |
1 (1.00) |
0.613 (1.00) |
NRAS | 15 (10%) | 140 |
0.131 (1.00) |
0.408 (1.00) |
0.531 (1.00) |
0.0659 (1.00) |
0.332 (1.00) |
1 (1.00) |
1 (1.00) |
PIK3CA | 26 (17%) | 129 |
0.252 (1.00) |
0.385 (1.00) |
0.0178 (1.00) |
0.218 (1.00) |
0.332 (1.00) |
1 (1.00) |
0.592 (1.00) |
SMAD4 | 18 (12%) | 137 |
0.212 (1.00) |
0.581 (1.00) |
0.01 (1.00) |
0.4 (1.00) |
0.495 (1.00) |
1 (1.00) |
1 (1.00) |
FAM123B | 19 (12%) | 136 |
0.168 (1.00) |
0.0336 (1.00) |
0.019 (1.00) |
0.579 (1.00) |
0.422 (1.00) |
0.498 (1.00) |
0.498 (1.00) |
TTN | 69 (45%) | 86 |
0.00599 (1.00) |
0.00803 (1.00) |
0.0011 (0.87) |
0.421 (1.00) |
0.653 (1.00) |
0.655 (1.00) |
0.793 (1.00) |
WBSCR17 | 17 (11%) | 138 |
0.48 (1.00) |
0.376 (1.00) |
0.388 (1.00) |
0.877 (1.00) |
0.305 (1.00) |
0.109 (1.00) |
0.109 (1.00) |
ACVR1B | 13 (8%) | 142 |
0.27 (1.00) |
0.46 (1.00) |
0.00744 (1.00) |
0.579 (1.00) |
0.331 (1.00) |
1 (1.00) |
0.386 (1.00) |
TNFRSF10C | 6 (4%) | 149 |
0.426 (1.00) |
1 (1.00) |
0.0811 (1.00) |
0.618 (1.00) |
0.169 (1.00) |
1 (1.00) |
1 (1.00) |
SMAD2 | 10 (6%) | 145 |
0.028 (1.00) |
0.233 (1.00) |
0.0333 (1.00) |
0.943 (1.00) |
0.377 (1.00) |
0.283 (1.00) |
1 (1.00) |
MAP2K4 | 9 (6%) | 146 |
0.485 (1.00) |
0.133 (1.00) |
0.0512 (1.00) |
0.446 (1.00) |
0.536 (1.00) |
1 (1.00) |
0.255 (1.00) |
PCBP1 | 4 (3%) | 151 |
0.385 (1.00) |
0.386 (1.00) |
0.486 (1.00) |
1 (1.00) |
1 (1.00) |
||
LRP1B | 30 (19%) | 125 |
0.00437 (1.00) |
0.00102 (0.814) |
0.00112 (0.89) |
0.0856 (1.00) |
0.0928 (1.00) |
1 (1.00) |
0.00789 (1.00) |
NRXN1 | 17 (11%) | 138 |
0.21 (1.00) |
0.208 (1.00) |
0.0134 (1.00) |
0.375 (1.00) |
0.771 (1.00) |
1 (1.00) |
0.455 (1.00) |
GRIA1 | 14 (9%) | 141 |
0.228 (1.00) |
0.103 (1.00) |
0.329 (1.00) |
0.0589 (1.00) |
0.47 (1.00) |
1 (1.00) |
0.000411 (0.33) |
SDK1 | 25 (16%) | 130 |
0.0158 (1.00) |
0.00187 (1.00) |
0.31 (1.00) |
0.125 (1.00) |
0.529 (1.00) |
1 (1.00) |
0.575 (1.00) |
SOX9 | 9 (6%) | 146 |
0.255 (1.00) |
0.436 (1.00) |
0.585 (1.00) |
0.14 (1.00) |
0.461 (1.00) |
1 (1.00) |
1 (1.00) |
DMD | 27 (17%) | 128 |
0.0222 (1.00) |
0.00627 (1.00) |
0.00855 (1.00) |
0.357 (1.00) |
0.0815 (1.00) |
1 (1.00) |
0.0998 (1.00) |
CNTN6 | 15 (10%) | 140 |
0.126 (1.00) |
0.162 (1.00) |
0.329 (1.00) |
0.833 (1.00) |
0.25 (1.00) |
1 (1.00) |
0.361 (1.00) |
GABRA5 | 8 (5%) | 147 |
0.663 (1.00) |
1 (1.00) |
1 (1.00) |
0.0749 (1.00) |
0.592 (1.00) |
0.197 (1.00) |
0.197 (1.00) |
OR2M4 | 8 (5%) | 147 |
0.00569 (1.00) |
0.259 (1.00) |
0.0771 (1.00) |
0.767 (1.00) |
0.817 (1.00) |
1 (1.00) |
0.255 (1.00) |
OR6N1 | 8 (5%) | 147 |
0.00206 (1.00) |
0.00822 (1.00) |
0.00971 (1.00) |
0.618 (1.00) |
1 (1.00) |
0.226 (1.00) |
1 (1.00) |
PCDH9 | 16 (10%) | 139 |
0.28 (1.00) |
0.711 (1.00) |
0.354 (1.00) |
0.847 (1.00) |
0.47 (1.00) |
1 (1.00) |
0.41 (1.00) |
TXNDC3 | 10 (6%) | 145 |
0.0949 (1.00) |
0.288 (1.00) |
0.0548 (1.00) |
0.523 (1.00) |
0.0878 (1.00) |
1 (1.00) |
0.283 (1.00) |
MGC26647 | 7 (5%) | 148 |
0.274 (1.00) |
0.796 (1.00) |
0.887 (1.00) |
1 (1.00) |
0.201 (1.00) |
1 (1.00) |
0.166 (1.00) |
FAM22F | 8 (5%) | 147 |
0.918 (1.00) |
0.272 (1.00) |
0.906 (1.00) |
0.345 (1.00) |
0.445 (1.00) |
1 (1.00) |
1 (1.00) |
ACVR2A | 8 (5%) | 147 |
0.0188 (1.00) |
0.337 (1.00) |
0.098 (1.00) |
0.167 (1.00) |
0.668 (1.00) |
1 (1.00) |
0.255 (1.00) |
TCF7L2 | 11 (7%) | 144 |
0.116 (1.00) |
0.815 (1.00) |
0.0875 (1.00) |
0.947 (1.00) |
1 (1.00) |
1 (1.00) |
0.283 (1.00) |
AFF2 | 15 (10%) | 140 |
0.0104 (1.00) |
0.0293 (1.00) |
0.648 (1.00) |
0.5 (1.00) |
0.123 (1.00) |
0.41 (1.00) |
0.41 (1.00) |
CNBD1 | 6 (4%) | 149 |
0.472 (1.00) |
0.773 (1.00) |
0.312 (1.00) |
1 (1.00) |
0.197 (1.00) |
||
OTOL1 | 7 (5%) | 148 |
0.385 (1.00) |
1 (1.00) |
1 (1.00) |
0.159 (1.00) |
1 (1.00) |
1 (1.00) |
0.226 (1.00) |
KCNA4 | 10 (6%) | 145 |
0.0778 (1.00) |
0.0895 (1.00) |
0.123 (1.00) |
0.0221 (1.00) |
0.039 (1.00) |
1 (1.00) |
1 (1.00) |
ISL1 | 8 (5%) | 147 |
0.0987 (1.00) |
0.389 (1.00) |
0.756 (1.00) |
0.767 (1.00) |
1 (1.00) |
1 (1.00) |
0.255 (1.00) |
MGC42105 | 10 (6%) | 145 |
0.00859 (1.00) |
0.103 (1.00) |
0.162 (1.00) |
0.266 (1.00) |
0.297 (1.00) |
1 (1.00) |
1 (1.00) |
ACOT4 | 3 (2%) | 152 |
0.676 (1.00) |
0.396 (1.00) |
0.736 (1.00) |
1 (1.00) |
1 (1.00) |
||
CDH11 | 13 (8%) | 142 |
0.132 (1.00) |
0.168 (1.00) |
0.258 (1.00) |
0.699 (1.00) |
0.266 (1.00) |
0.336 (1.00) |
1 (1.00) |
ATM | 21 (14%) | 134 |
0.116 (1.00) |
0.435 (1.00) |
0.00208 (1.00) |
0.306 (1.00) |
0.697 (1.00) |
1 (1.00) |
0.0702 (1.00) |
TPTE | 11 (7%) | 144 |
0.0132 (1.00) |
0.288 (1.00) |
0.129 (1.00) |
0.212 (1.00) |
0.668 (1.00) |
1 (1.00) |
0.31 (1.00) |
BTNL8 | 3 (2%) | 152 |
0.343 (1.00) |
0.396 (1.00) |
0.317 (1.00) |
0.531 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
KLHL4 | 12 (8%) | 143 |
0.00859 (1.00) |
0.202 (1.00) |
0.00618 (1.00) |
0.344 (1.00) |
1 (1.00) |
0.283 (1.00) |
0.283 (1.00) |
ROBO1 | 14 (9%) | 141 |
0.119 (1.00) |
0.0543 (1.00) |
0.0866 (1.00) |
0.205 (1.00) |
0.356 (1.00) |
1 (1.00) |
0.386 (1.00) |
GGT1 | 3 (2%) | 152 |
0.317 (1.00) |
1 (1.00) |
1 (1.00) |
||||
PCDHB2 | 13 (8%) | 142 |
0.0404 (1.00) |
0.0108 (1.00) |
0.0912 (1.00) |
0.388 (1.00) |
0.786 (1.00) |
1 (1.00) |
0.336 (1.00) |
POSTN | 11 (7%) | 144 |
0.27 (1.00) |
0.501 (1.00) |
0.0759 (1.00) |
0.618 (1.00) |
0.346 (1.00) |
1 (1.00) |
1 (1.00) |
OR51V1 | 9 (6%) | 146 |
0.00622 (1.00) |
0.00439 (1.00) |
0.00436 (1.00) |
1 (1.00) |
0.745 (1.00) |
1 (1.00) |
0.283 (1.00) |
GRIK3 | 14 (9%) | 141 |
0.33 (1.00) |
0.0396 (1.00) |
0.476 (1.00) |
0.464 (1.00) |
0.331 (1.00) |
1 (1.00) |
1 (1.00) |
LRRN3 | 9 (6%) | 146 |
0.0188 (1.00) |
0.0772 (1.00) |
0.288 (1.00) |
0.196 (1.00) |
0.208 (1.00) |
0.226 (1.00) |
1 (1.00) |
PRDM9 | 11 (7%) | 144 |
0.00152 (1.00) |
0.501 (1.00) |
0.129 (1.00) |
0.339 (1.00) |
1 (1.00) |
1 (1.00) |
0.336 (1.00) |
ADAM29 | 9 (6%) | 146 |
0.809 (1.00) |
0.354 (1.00) |
0.268 (1.00) |
0.531 (1.00) |
0.143 (1.00) |
1 (1.00) |
1 (1.00) |
KIAA1486 | 9 (6%) | 146 |
0.817 (1.00) |
0.631 (1.00) |
0.469 (1.00) |
0.405 (1.00) |
0.733 (1.00) |
1 (1.00) |
0.255 (1.00) |
PSG8 | 8 (5%) | 147 |
0.406 (1.00) |
0.511 (1.00) |
0.197 (1.00) |
0.461 (1.00) |
0.501 (1.00) |
0.226 (1.00) |
0.102 (1.00) |
NCKAP5 | 13 (8%) | 142 |
0.166 (1.00) |
0.0505 (1.00) |
0.143 (1.00) |
0.0165 (1.00) |
0.731 (1.00) |
1 (1.00) |
0.361 (1.00) |
C8B | 9 (6%) | 146 |
0.194 (1.00) |
0.174 (1.00) |
0.853 (1.00) |
0.73 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
CCDC160 | 5 (3%) | 150 |
0.521 (1.00) |
0.831 (1.00) |
0.506 (1.00) |
0.461 (1.00) |
1 (1.00) |
1 (1.00) |
0.166 (1.00) |
DCAF4L2 | 9 (6%) | 146 |
0.0567 (1.00) |
0.00439 (1.00) |
0.232 (1.00) |
0.618 (1.00) |
0.346 (1.00) |
1 (1.00) |
1 (1.00) |
DKK2 | 5 (3%) | 150 |
0.00642 (1.00) |
0.0245 (1.00) |
0.506 (1.00) |
0.108 (1.00) |
0.592 (1.00) |
1 (1.00) |
1 (1.00) |
EPHA3 | 13 (8%) | 142 |
0.00394 (1.00) |
0.0543 (1.00) |
0.258 (1.00) |
0.388 (1.00) |
0.786 (1.00) |
1 (1.00) |
0.361 (1.00) |
ERBB4 | 14 (9%) | 141 |
0.112 (1.00) |
0.165 (1.00) |
0.0538 (1.00) |
0.198 (1.00) |
0.0738 (1.00) |
1 (1.00) |
0.361 (1.00) |
GUCY1A3 | 10 (6%) | 145 |
0.171 (1.00) |
0.233 (1.00) |
0.227 (1.00) |
1 (1.00) |
0.668 (1.00) |
1 (1.00) |
0.283 (1.00) |
IFT80 | 7 (5%) | 148 |
0.155 (1.00) |
0.027 (1.00) |
0.135 (1.00) |
0.523 (1.00) |
0.501 (1.00) |
0.197 (1.00) |
1 (1.00) |
INHBA | 7 (5%) | 148 |
0.113 (1.00) |
0.25 (1.00) |
0.312 (1.00) |
0.919 (1.00) |
0.346 (1.00) |
0.166 (1.00) |
0.166 (1.00) |
KLK2 | 3 (2%) | 152 |
1 (1.00) |
0.198 (1.00) |
0.736 (1.00) |
1 (1.00) |
|||
LPPR4 | 11 (7%) | 144 |
0.132 (1.00) |
0.0111 (1.00) |
0.283 (1.00) |
0.0521 (1.00) |
0.297 (1.00) |
1 (1.00) |
1 (1.00) |
OR7C1 | 6 (4%) | 149 |
0.0296 (1.00) |
0.0379 (1.00) |
0.744 (1.00) |
1 (1.00) |
0.197 (1.00) |
||
SCN7A | 12 (8%) | 143 |
0.00115 (0.913) |
0.0116 (1.00) |
0.161 (1.00) |
0.339 (1.00) |
0.905 (1.00) |
1 (1.00) |
0.336 (1.00) |
TGFBR2 | 7 (5%) | 148 |
0.0293 (1.00) |
0.23 (1.00) |
0.0609 (1.00) |
0.515 (1.00) |
0.27 (1.00) |
0.197 (1.00) |
0.197 (1.00) |
TRPS1 | 13 (8%) | 142 |
0.0891 (1.00) |
0.233 (1.00) |
0.000547 (0.438) |
1 (1.00) |
0.821 (1.00) |
1 (1.00) |
0.336 (1.00) |
OR8J1 | 4 (3%) | 151 |
0.0844 (1.00) |
0.319 (1.00) |
0.619 (1.00) |
0.851 (1.00) |
1 (1.00) |
1 (1.00) |
0.103 (1.00) |
RIMS2 | 12 (8%) | 143 |
0.00804 (1.00) |
0.282 (1.00) |
0.0429 (1.00) |
0.167 (1.00) |
0.668 (1.00) |
1 (1.00) |
0.336 (1.00) |
SFMBT2 | 12 (8%) | 143 |
0.45 (1.00) |
0.259 (1.00) |
0.21 (1.00) |
0.0986 (1.00) |
1 (1.00) |
1 (1.00) |
0.361 (1.00) |
IL18R1 | 8 (5%) | 147 |
0.286 (1.00) |
0.259 (1.00) |
0.294 (1.00) |
0.767 (1.00) |
0.817 (1.00) |
1 (1.00) |
0.255 (1.00) |
PCDH17 | 14 (9%) | 141 |
0.347 (1.00) |
0.927 (1.00) |
0.673 (1.00) |
0.631 (1.00) |
0.329 (1.00) |
1 (1.00) |
0.361 (1.00) |
FLRT2 | 11 (7%) | 144 |
0.68 (1.00) |
0.789 (1.00) |
0.367 (1.00) |
0.592 (1.00) |
0.786 (1.00) |
1 (1.00) |
0.283 (1.00) |
PTEN | 4 (3%) | 151 |
0.017 (1.00) |
0.688 (1.00) |
0.132 (1.00) |
1 (1.00) |
0.135 (1.00) |
||
ZFHX4 | 17 (11%) | 138 |
0.516 (1.00) |
0.376 (1.00) |
0.455 (1.00) |
0.517 (1.00) |
0.529 (1.00) |
1 (1.00) |
0.0452 (1.00) |
NRXN3 | 15 (10%) | 140 |
0.00109 (0.869) |
0.0385 (1.00) |
0.0506 (1.00) |
0.631 (1.00) |
0.25 (1.00) |
1 (1.00) |
0.386 (1.00) |
LIFR | 13 (8%) | 142 |
0.0325 (1.00) |
0.578 (1.00) |
0.355 (1.00) |
0.723 (1.00) |
0.445 (1.00) |
1 (1.00) |
0.0253 (1.00) |
ZNF429 | 7 (5%) | 148 |
0.0908 (1.00) |
0.511 (1.00) |
0.887 (1.00) |
0.618 (1.00) |
0.592 (1.00) |
1 (1.00) |
0.197 (1.00) |
OR2M2 | 6 (4%) | 149 |
0.406 (1.00) |
1 (1.00) |
0.574 (1.00) |
0.442 (1.00) |
0.397 (1.00) |
1 (1.00) |
0.166 (1.00) |
TMEM132D | 15 (10%) | 140 |
0.000353 (0.284) |
0.000781 (0.624) |
0.0272 (1.00) |
0.101 (1.00) |
0.329 (1.00) |
1 (1.00) |
1 (1.00) |
SAT1 | 4 (3%) | 151 |
0.00392 (1.00) |
0.071 (1.00) |
0.619 (1.00) |
0.531 (1.00) |
0.143 (1.00) |
1 (1.00) |
1 (1.00) |
CDH18 | 10 (6%) | 145 |
0.0179 (1.00) |
0.165 (1.00) |
0.0471 (1.00) |
0.122 (1.00) |
0.298 (1.00) |
1 (1.00) |
0.283 (1.00) |
P2RY10 | 6 (4%) | 149 |
0.328 (1.00) |
0.442 (1.00) |
0.744 (1.00) |
0.523 (1.00) |
0.501 (1.00) |
1 (1.00) |
1 (1.00) |
SYT16 | 6 (4%) | 149 |
0.0293 (1.00) |
0.101 (1.00) |
0.0596 (1.00) |
0.314 (1.00) |
0.673 (1.00) |
0.197 (1.00) |
1 (1.00) |
DKK4 | 4 (3%) | 151 |
0.071 (1.00) |
0.071 (1.00) |
0.188 (1.00) |
0.176 (1.00) |
0.397 (1.00) |
1 (1.00) |
1 (1.00) |
NALCN | 14 (9%) | 141 |
0.012 (1.00) |
0.092 (1.00) |
0.0129 (1.00) |
0.474 (1.00) |
0.771 (1.00) |
1 (1.00) |
0.361 (1.00) |
SULT1C4 | 3 (2%) | 152 |
0.0124 (1.00) |
0.027 (1.00) |
0.0684 (1.00) |
1 (1.00) |
|||
UMOD | 7 (5%) | 148 |
0.117 (1.00) |
0.136 (1.00) |
0.166 (1.00) |
0.347 (1.00) |
0.0961 (1.00) |
1 (1.00) |
0.135 (1.00) |
CPXCR1 | 6 (4%) | 149 |
0.071 (1.00) |
0.151 (1.00) |
0.574 (1.00) |
0.478 (1.00) |
1 (1.00) |
0.197 (1.00) |
0.0141 (1.00) |
PDZRN4 | 12 (8%) | 143 |
0.00509 (1.00) |
0.00295 (1.00) |
0.00593 (1.00) |
0.0425 (1.00) |
0.168 (1.00) |
0.31 (1.00) |
0.31 (1.00) |
USP17L2 | 7 (5%) | 148 |
0.329 (1.00) |
0.337 (1.00) |
0.744 (1.00) |
0.135 (1.00) |
0.318 (1.00) |
0.197 (1.00) |
0.197 (1.00) |
ESR1 | 11 (7%) | 144 |
0.135 (1.00) |
0.0736 (1.00) |
0.105 (1.00) |
0.515 (1.00) |
0.0961 (1.00) |
1 (1.00) |
0.283 (1.00) |
FAM5C | 10 (6%) | 145 |
0.118 (1.00) |
0.389 (1.00) |
0.0471 (1.00) |
0.284 (1.00) |
0.297 (1.00) |
0.283 (1.00) |
0.283 (1.00) |
MIER3 | 10 (6%) | 145 |
0.000875 (0.698) |
0.00803 (1.00) |
0.00303 (1.00) |
0.569 (1.00) |
1 (1.00) |
1 (1.00) |
0.31 (1.00) |
NLRP5 | 10 (6%) | 145 |
0.0259 (1.00) |
0.732 (1.00) |
0.162 (1.00) |
0.405 (1.00) |
0.231 (1.00) |
1 (1.00) |
0.255 (1.00) |
OR6T1 | 6 (4%) | 149 |
0.934 (1.00) |
0.59 (1.00) |
0.744 (1.00) |
0.737 (1.00) |
1 (1.00) |
0.166 (1.00) |
1 (1.00) |
PCDH10 | 14 (9%) | 141 |
0.136 (1.00) |
0.162 (1.00) |
0.237 (1.00) |
0.579 (1.00) |
0.541 (1.00) |
1 (1.00) |
0.361 (1.00) |
PCDHB5 | 12 (8%) | 143 |
0.087 (1.00) |
0.282 (1.00) |
0.161 (1.00) |
0.177 (1.00) |
0.0126 (1.00) |
1 (1.00) |
0.31 (1.00) |
TRPC6 | 8 (5%) | 147 |
0.105 (1.00) |
0.796 (1.00) |
0.35 (1.00) |
0.618 (1.00) |
0.592 (1.00) |
1 (1.00) |
0.197 (1.00) |
RHOA | 4 (3%) | 151 |
0.619 (1.00) |
1 (1.00) |
1 (1.00) |
0.135 (1.00) |
1 (1.00) |
||
CYTL1 | 4 (3%) | 151 |
0.287 (1.00) |
0.776 (1.00) |
0.619 (1.00) |
1 (1.00) |
0.135 (1.00) |
||
CHRM2 | 8 (5%) | 147 |
0.472 (1.00) |
0.25 (1.00) |
0.138 (1.00) |
0.405 (1.00) |
0.733 (1.00) |
0.226 (1.00) |
0.226 (1.00) |
GALNT14 | 9 (6%) | 146 |
0.177 (1.00) |
0.541 (1.00) |
0.0807 (1.00) |
0.685 (1.00) |
0.0586 (1.00) |
1 (1.00) |
0.226 (1.00) |
LRRIQ3 | 7 (5%) | 148 |
0.635 (1.00) |
0.433 (1.00) |
0.47 (1.00) |
0.523 (1.00) |
0.364 (1.00) |
1 (1.00) |
0.226 (1.00) |
NAALAD2 | 11 (7%) | 144 |
0.0262 (1.00) |
0.0381 (1.00) |
0.0127 (1.00) |
0.0972 (1.00) |
0.0154 (1.00) |
1 (1.00) |
0.283 (1.00) |
PCDH11X | 11 (7%) | 144 |
0.102 (1.00) |
0.501 (1.00) |
0.129 (1.00) |
0.108 (1.00) |
0.217 (1.00) |
1 (1.00) |
0.31 (1.00) |
TFAP2D | 5 (3%) | 150 |
0.582 (1.00) |
0.864 (1.00) |
0.506 (1.00) |
0.804 (1.00) |
0.673 (1.00) |
1 (1.00) |
1 (1.00) |
TNR | 15 (10%) | 140 |
0.0139 (1.00) |
0.0253 (1.00) |
0.00125 (0.991) |
0.197 (1.00) |
0.298 (1.00) |
1 (1.00) |
1 (1.00) |
CNTNAP4 | 10 (6%) | 145 |
0.0102 (1.00) |
0.688 (1.00) |
0.0226 (1.00) |
0.425 (1.00) |
0.733 (1.00) |
0.283 (1.00) |
0.0325 (1.00) |
DOCK2 | 16 (10%) | 139 |
0.00245 (1.00) |
0.00388 (1.00) |
0.00754 (1.00) |
0.889 (1.00) |
0.412 (1.00) |
1 (1.00) |
0.433 (1.00) |
P value = 5.58e-06 (Fisher's exact test), Q value = 0.0045
Table S1. Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 30 | 58 | 29 | 24 |
BRAF MUTATED | 12 | 1 | 4 | 1 |
BRAF WILD-TYPE | 18 | 57 | 25 | 23 |
Figure S1. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'
![](D2V1.png)
P value = 8.43e-08 (Fisher's exact test), Q value = 6.9e-05
Table S2. Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 53 | 43 | 45 |
BRAF MUTATED | 1 | 16 | 1 |
BRAF WILD-TYPE | 52 | 27 | 44 |
Figure S2. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'
![](D2V2.png)
P value = 8.5e-05 (Fisher's exact test), Q value = 0.069
Table S3. Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 70 | 64 | 11 | 8 |
BRAF MUTATED | 2 | 18 | 0 | 0 |
BRAF WILD-TYPE | 68 | 46 | 11 | 8 |
Figure S3. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'
![](D2V3.png)
P value = 1.08e-09 (Fisher's exact test), Q value = 8.8e-07
Table S4. Gene #7: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 70 | 64 | 11 | 8 |
TP53 MUTATED | 51 | 13 | 4 | 6 |
TP53 WILD-TYPE | 19 | 51 | 7 | 2 |
Figure S4. Get High-res Image Gene #7: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'
![](D7V3.png)
P value = 0.000172 (Fisher's exact test), Q value = 0.14
Table S5. Gene #17: 'FAT4 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 70 | 64 | 11 | 8 |
FAT4 MUTATED | 4 | 22 | 1 | 1 |
FAT4 WILD-TYPE | 66 | 42 | 10 | 7 |
Figure S5. Get High-res Image Gene #17: 'FAT4 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'
![](D17V3.png)
P value = 0.000232 (Fisher's exact test), Q value = 0.19
Table S6. Gene #48: 'FLG MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 30 | 58 | 29 | 24 |
FLG MUTATED | 10 | 2 | 8 | 2 |
FLG WILD-TYPE | 20 | 56 | 21 | 22 |
Figure S6. Get High-res Image Gene #48: 'FLG MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'
![](D48V1.png)
P value = 0.00027 (Fisher's exact test), Q value = 0.22
Table S7. Gene #48: 'FLG MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 70 | 64 | 11 | 8 |
FLG MUTATED | 3 | 18 | 1 | 3 |
FLG WILD-TYPE | 67 | 46 | 10 | 5 |
Figure S7. Get High-res Image Gene #48: 'FLG MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'
![](D48V3.png)
P value = 4.26e-06 (Fisher's exact test), Q value = 0.0035
Table S8. Gene #60: 'DNAH5 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 30 | 58 | 29 | 24 |
DNAH5 MUTATED | 13 | 4 | 9 | 0 |
DNAH5 WILD-TYPE | 17 | 54 | 20 | 24 |
Figure S8. Get High-res Image Gene #60: 'DNAH5 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'
![](D60V1.png)
P value = 1.21e-05 (Fisher's exact test), Q value = 0.0098
Table S9. Gene #61: 'CASP8 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 53 | 43 | 45 |
CASP8 MUTATED | 0 | 9 | 0 |
CASP8 WILD-TYPE | 53 | 34 | 45 |
Figure S9. Get High-res Image Gene #61: 'CASP8 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'
![](D61V2.png)
P value = 0.000266 (Fisher's exact test), Q value = 0.21
Table S10. Gene #82: 'ZC3H13 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 53 | 43 | 45 |
ZC3H13 MUTATED | 3 | 12 | 1 |
ZC3H13 WILD-TYPE | 50 | 31 | 44 |
Figure S10. Get High-res Image Gene #82: 'ZC3H13 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'
![](D82V2.png)
P value = 0.000146 (Fisher's exact test), Q value = 0.12
Table S11. Gene #110: 'SYNE1 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 30 | 58 | 29 | 24 |
SYNE1 MUTATED | 13 | 7 | 14 | 3 |
SYNE1 WILD-TYPE | 17 | 51 | 15 | 21 |
Figure S11. Get High-res Image Gene #110: 'SYNE1 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'
![](D110V1.png)
P value = 0.000289 (Fisher's exact test), Q value = 0.23
Table S12. Gene #110: 'SYNE1 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 70 | 64 | 11 | 8 |
SYNE1 MUTATED | 9 | 26 | 0 | 1 |
SYNE1 WILD-TYPE | 61 | 38 | 11 | 7 |
Figure S12. Get High-res Image Gene #110: 'SYNE1 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'
![](D110V3.png)
-
Mutation data file = COAD-TP.mutsig.cluster.txt
-
Molecular subtypes file = COAD-TP.transferedmergedcluster.txt
-
Number of patients = 155
-
Number of significantly mutated genes = 120
-
Number of Molecular subtypes = 7
-
Exclude genes that fewer than K tumors have mutations, K = 3
For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R
For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.